The efforts described above are expected to yield a well-supported
phylogeny of green plants. This will be used, alone and in combination
with other phylogenetic information, to make a variety of evolutionary
inferences. Specifically we will focus on the evolution of a set
of morphological characters, on patterns of molecular evolution,
and on rates of diversification. Meaningful answers to these questions
require large taxon sampling. Tree size is a critical factor with
respect to the ability to distinguish between competing evolutionary
models, such as symmetrical versus asymmetrical probabilities of
character change (e.g., [138, 139]) and correlated character evolution
(e.g., [140]). As a result of the concatenation analyses discussed
in the previous section, we anticipate the assembly of phylogenetic
hypotheses large and well-supported enough to ensure coverage of
the groups that are necessary to address specific evolutionary hypothesis,
and to allow statistically meaningful comparative analyses.

Our studies of character evolution will focus initially on issues
of broad evolutionary significance from the standpoint of the entire
Tree of Life. Specifically, basal green plants will allow analyses
of (1) the origins of multicellularity, (2) transitions to life
on land, and (3) the evolution of an exceptionally wide variety
of life cycles. (1) Multicellularity appears to have evolved repeatedly
within green plants. In the streptophyte clade, multicellularity
preceded the evolution of embryophyte land plants. In chlorophytes
there have been multiple paths to multicellularity, including colonial
forms in the volvocine line, multiple origins of filamentous and
more complex parenchymatous plant bodies in Chlorophyceae and Ulvophyceae,
and siphonous forms culminating in coenocytic thalli within Ulvophyceae.
(2) Transitions to life on land also occurred repeatedly early in
green plant evolution. The embrophytes represent one such occurrence,
but multiple independent events are apparent within Trebouxiophyceae
(see Chapman et al., 1998), often entailing symbiotic relationships
with fungi and animals. (3) Regarding life cycle evolution, great
interest has focused on the transitions that preceded embryophyte
evolution, and the subsequent origination of alternation of gametophyte
and sporophyte generations. Of equal evolutionary interest are many
apparent shifts within chlorophytes, including the evolution of
animal-like life cycles (diploid dominance, products of meiosis
functioning as gametes) in Codium and other Ulvophyceae.

In each of these cases, and others related to ultrastructural
features and genome evolution, we will infer ancestral states and
evolutionary sequences using parsimony and maximum likelihood approaches
(see [141, 142, 138, 139, 143-145] To test for the correlated evolution
of characters we will employ a battery of comparative techniques,
again using parsimony, likelihood, and Bayesian methods (e.g., [146-
150]), and performing relevant sensitivity analyses (e.g., [151,
152]).

Finally, we will focus on issues concerning the tempo of green
plant evolution. The absolute time of key divergences will be inferred
using molecular data, calibrated by the placement of fossils (see
letter from A. Knoll). Methods that variously relax the molecular
clock assumption will be used, including penalized likelihood and
Bayesian methods, in which fossil evidence places minimum and maximum
bounds on the estimates [153-160]. We will also use a variety of
methods to assess if and when shifts in diversification rate occurred
in basal green phylogeny (reviewed in [161-163]), and explore correlations
between diversification shifts, character changes, and rates of
molecular evolution (e.g., [164]).